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1y5y

Structure of the tetrahydromethanopterin dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Formaldehyde-activating enzyme fae

Methylobacterium extorquens

UniProt Q9FA38

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 5 CALCIUM ION × 1 SODIUM ION × 2 water × 5 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 10 CALCIUM ION × 2 SODIUM ION × 4 water × 10 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers
1y5y 1y5y 1y60

3 assemblies

Heteromeric or nucleic-acid complex
8ub7 8ub8 8ub9 8uba 8ubb 8ubc 8ubd 8ube 8ubf

9 assemblies

View Construct and Data Evidence
UniProt name FAE_METEX
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–169； UniProt 1–169 Author chain B； PDBConstruct 1–169； UniProt 1–169 Author chain C； PDBConstruct 1–169； UniProt 1–169 Author chain D； PDBConstruct 1–169； UniProt 1–169 Author chain E； PDBConstruct 1–169； UniProt 1–169

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id1y5y
Deposition date deposition_date2004-12-03
Structure title titleStructure of the tetrahydromethanopterin dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1
Keywords keywordsPentamer, beta-alpha-beta left handed crossover, flexible C-terminus, LYASE; LYASE
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1y5y__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1y5y__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1y5y__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）26.84 Å
Rg (electron density)25.70 Å
Total Rg26.56 Å
Atom count5976
Residues797
Excluded volume106540 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1y5y__assembly_1__model_1 pentameric （5） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1y5y__assembly_2__model_1 decameric （10） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd1y5ya_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamilyd.14.1 — Ribosomal protein S5 domain 2-like
Family Family familyd.14.1.12 — Formaldehyde-activating enzyme, FAE
Domain ID domain_idd1y5yb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamilyd.14.1 — Ribosomal protein S5 domain 2-like
Family Family familyd.14.1.12 — Formaldehyde-activating enzyme, FAE
Domain ID domain_idd1y5yc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamilyd.14.1 — Ribosomal protein S5 domain 2-like
Family Family familyd.14.1.12 — Formaldehyde-activating enzyme, FAE
Domain ID domain_idd1y5yd_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamilyd.14.1 — Ribosomal protein S5 domain 2-like
Family Family familyd.14.1.12 — Formaldehyde-activating enzyme, FAE
Domain ID domain_idd1y5ye_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamilyd.14.1 — Ribosomal protein S5 domain 2-like
Family Family familyd.14.1.12 — Formaldehyde-activating enzyme, FAE

CATH v4.4 (5 domains)

Domain ID domain_id1y5yA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily60 — Formaldehyde-activating enzyme
Domain ID domain_id1y5yB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily60 — Formaldehyde-activating enzyme
Domain ID domain_id1y5yC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily60 — Formaldehyde-activating enzyme
Domain ID domain_id1y5yD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily60 — Formaldehyde-activating enzyme
Domain ID domain_id1y5yE00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily60 — Formaldehyde-activating enzyme
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7. Citations (1)